bio-data-visualization-sequence-logos
Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.
npx skills add BioTender-max/awesome-bio-agent-skills --skill sequence-logos --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: ggseqlogo 0.2 (CRAN; per Wagih 2017), Logomaker 0.8+ (Python), WebLogo 3.7+ (CLI), Biopython 1.83+ (motif parsing), MEME suite 5.5+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Sequence Logos **"Plot a sequence motif"** -> Render a per-position stack of letters whose total height encodes information content (Schneider-Stephens 1990 *Nucleic Acids Res* 18:6097) and individual letter height is proportional to base/aa frequency. The information-content encoding makes conserved positions visually tall and variable positions visually short — the visual is *the conservation profile*. - R: `ggseqlogo::ggseqlogo` (Wagih 2017 *Bioinformatics* 33:3645) - Python: `logomaker.Logo` - CLI: `weblogo` (Crooks 2004 *Genome Res* 14:1188) ## The Single Most Important Modern Insight -- Bits vs Probability Are Different V
- Version Compatibility
- Decision Tree by Use Case
- ggseqlogo (R) -- Canonical Bioinformatics Default
- Logomaker (Python) -- Most Flexible
- WebLogo (CLI / web)
- Background Composition Correction
- Per-Method Failure Modes
- Probability encoding mistaken for bits
- Background uniform when genome composition matters
- PWM rows/columns reversed
- Custom alphabet not recognized
- Aligned sequences of unequal length
- Logo for too few input sequences
- Stacked logos with different alphabets compared
weblogo --format pdf --sequence-type dna \
What does the bio-data-visualization-sequence-logos skill do?
Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill sequence-logos --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.